Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014648.1 Kokia drynarioides strain JFW-HI SEQ_129687, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 363951
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:284407 original size:14 final size:14
Alignment explanation
Indices: 284388--284434 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
284378 AAAGTTAACG
284388 ATCAACGGTCAACT
1 ATCAACGGTCAACT
**
284402 ATCAACTATCAA-T
1 ATCAACGGTCAACT
*
284415 AGTCAATGGTCAACT
1 A-TCAACGGTCAACT
284430 ATCAA
1 ATCAA
284435 TGATCAACGG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (14 bp):
ATCAACGGTCAACT
Found at i:284419 original size:21 final size:21
Alignment explanation
Indices: 284395--284483 Score: 76
Period size: 21 Copynumber: 4.2 Consensus size: 21
284385 ACGATCAACG
284395 GTCAACTATCAACTATCAATA
1 GTCAACTATCAACTATCAATA
*
284416 GTCAA-TGGTCAACTATCAAT-
1 GTCAACT-ATCAACTATCAATA
** *
284436 GATCAACGGTGAACTATCAATA
1 G-TCAACTATCAACTATCAATA
*
284458 GTCAACAATCAAC-ACTCAATGA
1 GTCAACTATCAACTA-TCAAT-A
284480 GTCA
1 GTCA
284484 GATTCGATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.05
21 47 0.84
22 6 0.11
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.25
Consensus pattern (21 bp):
GTCAACTATCAACTATCAATA
Found at i:284435 original size:14 final size:14
Alignment explanation
Indices: 284396--284442 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
284386 CGATCAACGG
284396 TCAACTATCAACT-A
1 TCAACTATCAA-TGA
*
284410 TCAA-TAGTCAATGG
1 TCAACTA-TCAATGA
284424 TCAACTATCAATGA
1 TCAACTATCAATGA
284438 TCAAC
1 TCAAC
284443 GGTGAACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 23 0.82
15 2 0.07
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (14 bp):
TCAACTATCAATGA
Found at i:288895 original size:21 final size:21
Alignment explanation
Indices: 288871--288910 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
288861 AACAATATAA
288871 TGGTTTT-ACCTTTTAACTTAG
1 TGGTTTTGA-CTTTTAACTTAG
288892 TGGTTTTGACTTTTAACTT
1 TGGTTTTGACTTTTAACTT
288911 GATGAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.55
Consensus pattern (21 bp):
TGGTTTTGACTTTTAACTTAG
Found at i:289147 original size:23 final size:21
Alignment explanation
Indices: 289116--289161 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
289106 AATACCTTGA
289116 TTAACTCAAATAACTTGAATTAT
1 TTAACTC-AA-AACTTGAATTAT
* *
289139 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAACTTGAATTAT
289160 TT
1 TT
289162 TTCGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAACTTGAATTAT
Found at i:290075 original size:18 final size:16
Alignment explanation
Indices: 290031--290081 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
290021 TGAAAACTTT
* *
290031 AAAATATATAA-TTCA
1 AAAATATAAAATTTAA
290046 AAAATATAAAATTATAA
1 AAAATATAAAATT-TAA
*
290063 AAAATTATTAAATTTAA
1 AAAA-TATAAAATTTAA
290080 AA
1 AA
290082 TTATTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 10 0.33
16 1 0.03
17 11 0.37
18 8 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATAAAATTTAA
Found at i:290149 original size:39 final size:40
Alignment explanation
Indices: 290047--290150 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 40
290037 TATAATTCAA
*
290047 AAATATAAAATTATAAAAAATTATTAAATTTAAAATTATTTAT
1 AAATAT-AAATTATAAAAAA-TATT-AATATAAAATTATTTAT
** *
290090 AATATATAAATCCTAAAAAATATT-ATATAAAA-TATTTTT
1 AA-ATATAAATTATAAAAAATATTAATATAAAATTATTTAT
*
290129 ATAATATAAATTATATAAAATA
1 A-AATATAAATTATAAAAAATA
290151 AAAATAATTC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
39 23 0.44
40 8 0.15
42 4 0.08
43 13 0.25
44 4 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (40 bp):
AAATATAAATTATAAAAAATATTAATATAAAATTATTTAT
Found at i:295578 original size:11 final size:11
Alignment explanation
Indices: 295564--295590 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
295554 CATTATCCTT
295564 ATATTATAATA
1 ATATTATAATA
295575 ATATTATAATA
1 ATATTATAATA
295586 ATATT
1 ATATT
295591 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATTATAATA
Found at i:295771 original size:17 final size:17
Alignment explanation
Indices: 295749--295786 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
295739 CTGACTCCAT
*
295749 TTTTAT-TTTCTAGTTTA
1 TTTTATATTT-TAGTATA
295766 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
295783 TTTT
1 TTTT
295787 TCATCTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:296087 original size:27 final size:28
Alignment explanation
Indices: 296049--296110 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
296039 AAATGAGTGG
*
296049 AATAAATAGTTCTAAGTATTA-AATATA
1 AATAAATAGTTCTAACTATTATAATATA
* *
296076 AATAATTAGTTCTAACTATTATACTATA
1 AATAAATAGTTCTAACTATTATAATATA
296104 AA-AAATA
1 AATAAATA
296111 ATTAATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (28 bp):
AATAAATAGTTCTAACTATTATAATATA
Found at i:297470 original size:2 final size:2
Alignment explanation
Indices: 297463--297498 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
297453 TGTCATTGTT
297463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
297499 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:297562 original size:29 final size:29
Alignment explanation
Indices: 297523--297618 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 29
297513 AAAAACACTA
297523 CTTTAAATAAATCTTGCATTAATGAATAT
1 CTTTAAATAAATCTTGCATTAATGAATAT
* * *
297552 CTTTACATAAATC-T---TTAA-CACTA-
1 CTTTAAATAAATCTTGCATTAATGAATAT
297575 CTTTAAATAAATCTTGCATTAATGAATAT
1 CTTTAAATAAATCTTGCATTAATGAATAT
*
297604 CTTTACATAAATCTT
1 CTTTAAATAAATCTT
297619 TCTTCATTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
23 12 0.22
24 4 0.07
25 4 0.07
27 4 0.07
28 4 0.07
29 26 0.48
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42
Consensus pattern (29 bp):
CTTTAAATAAATCTTGCATTAATGAATAT
Found at i:297573 original size:52 final size:52
Alignment explanation
Indices: 297516--297619 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
297506 AATAATTAAA
297516 AACACTACTTTAAATAAATCTTGCATTAATGAATATCTTTACATAAATCTTT
1 AACACTACTTTAAATAAATCTTGCATTAATGAATATCTTTACATAAATCTTT
297568 AACACTACTTTAAATAAATCTTGCATTAATGAATATCTTTACATAAATCTTT
1 AACACTACTTTAAATAAATCTTGCATTAATGAATATCTTTACATAAATCTTT
297620 CTTCATTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (52 bp):
AACACTACTTTAAATAAATCTTGCATTAATGAATATCTTTACATAAATCTTT
Found at i:300000 original size:55 final size:55
Alignment explanation
Indices: 299934--300226 Score: 363
Period size: 55 Copynumber: 5.3 Consensus size: 55
299924 GAGTTATAGA
* *
299934 AGGCACATGGGCTGGCACACGGGCGTGTGT-TAGGATGTGTGTGTATACTGTTAGG
1 AGGCACATGGGCTGGCACACGGGCGTGTGTCAAGG-TGTGTGTGTATACTGTTTGG
* *
299989 AGGCACATGGGCTGGCACATGGGCGTATGTCAAGGTGTGTGTGTATACTGTTTGG
1 AGGCACATGGGCTGGCACACGGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTGG
* * * * *
300044 AGGTACATGAGCTGGCACACGGGAGTGTGTCAAGGTGTATGTGTATACTGTTTGA
1 AGGCACATGGGCTGGCACACGGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTGG
* * * *
300099 AGGCACATGGGCTGGTACACGGGCGTGTGCCAAGGTGTGTGTGTGTGTGTACTATTTGG
1 AGGCACATGGGCTGGCACACGGGCGTGTGTCAA---G-GTGTGTGTGTATACTGTTTGG
* ** * * *
300158 AGGTACACAGGCTGGTACACGGGCGTGTGTCAAGGTGTGTGTGTATGCTATTTGG
1 AGGCACATGGGCTGGCACACGGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTGG
300213 AGGCACATGGGCTG
1 AGGCACATGGGCTG
300227 ACATAAAAAA
Statistics
Matches: 204, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
55 153 0.75
56 4 0.02
58 1 0.00
59 46 0.23
ACGTcount: A:0.19, C:0.15, G:0.39, T:0.28
Consensus pattern (55 bp):
AGGCACATGGGCTGGCACACGGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTGG
Found at i:300072 original size:110 final size:112
Alignment explanation
Indices: 299938--300226 Score: 370
Period size: 114 Copynumber: 2.6 Consensus size: 112
299928 TATAGAAGGC
* * *
299938 ACATGGGCTGGCACACGGGCGTGTGT-TAGGATGTGTGTGTATACTGTTAGGAGGCACATGGGCT
1 ACATGAGCTGGCACACGGGCGTGTGTCAAGG-TGTGTGTGTATACTGTTTGGAGGCACATGGGCT
* * *
300002 GGCACATGGGCGTATGTCAA-G-GTGTGTGTGTATACTGTTTGGAGGT
65 GGCACACGGGCGTATGCCAAGGTGTGTGTGTGTATACTATTTGGAGGT
* * *
300048 ACATGAGCTGGCACACGGGAGTGTGTCAAGGTGTATGTGTATACTGTTTGAAGGCACATGGGCTG
1 ACATGAGCTGGCACACGGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTGGAGGCACATGGGCTG
* * *
300113 GTACACGGGCGTGTGCCAAGGTGTGTGTGTGTGTGTACTATTTGGAGGT
66 GCACACGGGCGTATGCCAA-G-GTGTGTGTGTGTATACTATTTGGAGGT
* * * *
300162 ACA-CAGGCTGGTACACGGGCGTGTGTCAAGGTGTGTGTGTATGCTATTTGGAGGCACATGGGCT
1 ACATGA-GCTGGCACACGGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTGGAGGCACATGGGCT
300226 G
65 G
300227 ACATAAAAAA
Statistics
Matches: 154, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
110 70 0.45
111 3 0.02
113 2 0.01
114 79 0.51
ACGTcount: A:0.19, C:0.15, G:0.38, T:0.28
Consensus pattern (112 bp):
ACATGAGCTGGCACACGGGCGTGTGTCAAGGTGTGTGTGTATACTGTTTGGAGGCACATGGGCTG
GCACACGGGCGTATGCCAAGGTGTGTGTGTGTATACTATTTGGAGGT
Found at i:309912 original size:20 final size:20
Alignment explanation
Indices: 309871--309912 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
309861 TTGTTTTCAA
* *
309871 TTTATTTATTTCATTTTATT
1 TTTATTTATTTAATATTATT
309891 TTTATTTAGTTTAATATT-TT
1 TTTATTTA-TTTAATATTATT
309911 TT
1 TT
309913 ATCACTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTATTTATTTAATATTATT
Found at i:311460 original size:11 final size:11
Alignment explanation
Indices: 311446--311488 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
311436 AGTTAAATAT
311446 TATTTTATTAA
1 TATTTTATTAA
311457 TATTTTACTTAA
1 TATTTTA-TTAA
311469 -ATATTTATTAA
1 TAT-TTTATTAA
311480 TATTTTATT
1 TATTTTATT
311489 TAGAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:331770 original size:13 final size:13
Alignment explanation
Indices: 331736--331793 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
331726 TACATATATT
*
331736 TTTCACATAACCA
1 TTTCATATAACCA
* *
331749 TTCCTTATAACCA
1 TTTCATATAACCA
* *
331762 TTTCATATAATCG
1 TTTCATATAACCA
* *
331775 TTTCATTTTACCA
1 TTTCATATAACCA
331788 TTTCAT
1 TTTCAT
331794 TTACATATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (13 bp):
TTTCATATAACCA
Found at i:334080 original size:13 final size:13
Alignment explanation
Indices: 334062--334095 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
334052 TCTACAAATG
334062 CTTCATATAAACA
1 CTTCATATAAACA
*
334075 CTTCATATAATCA
1 CTTCATATAAACA
*
334088 TTTCATAT
1 CTTCATAT
334096 GTTTATTCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (13 bp):
CTTCATATAAACA
Found at i:335393 original size:21 final size:21
Alignment explanation
Indices: 335352--335407 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
335342 CTACAGAATC
*
335352 CTACCGATAGAACTAGTAGTT
1 CTACCGATACAACTAGTAGTT
*
335373 CTACCGATACAAGTA-TGAGTT
1 CTACCGATACAACTAGT-AGTT
* *
335394 ATACTGATACAACT
1 CTACCGATACAACT
335408 CAGACAACTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
CTACCGATACAACTAGTAGTT
Found at i:336179 original size:13 final size:13
Alignment explanation
Indices: 336145--336202 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
336135 TACATATATT
*
336145 TTTCACATAACCA
1 TTTCATATAACCA
* *
336158 TTCCTTATAACCA
1 TTTCATATAACCA
**
336171 TTTCATATAACTG
1 TTTCATATAACCA
* *
336184 TTTCATTTTACCA
1 TTTCATATAACCA
336197 TTTCAT
1 TTTCAT
336203 TTACGTATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (13 bp):
TTTCATATAACCA
Found at i:337151 original size:28 final size:27
Alignment explanation
Indices: 337044--337173 Score: 127
Period size: 28 Copynumber: 4.6 Consensus size: 27
337034 TTCATTTTCA
* * *
337044 ACCTTTTCATTTATTATCCTTCTAGATAAT
1 ACCTTTTCA-ATAATATCCTT-TCGAT-AT
* * *
337074 ATCCTTTTCAAAAATATCCTTTTGGGTAT
1 A-CCTTTTCAATAATATCC-TTTCGATAT
337103 ACCTTTT-AATAATATCCTTTCGTATAT
1 ACCTTTTCAATAATATCCTTTCG-ATAT
*
337130 ACCTTTTCAATTATATCCTTTCGAATAT
1 ACCTTTTCAATAATATCCTTTCG-ATAT
337158 ACCTTTTCAATAATAT
1 ACCTTTTCAATAATAT
337174 ATTAAAGCAT
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
26 4 0.05
27 19 0.22
28 39 0.46
29 3 0.04
30 10 0.12
31 10 0.12
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (27 bp):
ACCTTTTCAATAATATCCTTTCGATAT
Found at i:337169 original size:13 final size:13
Alignment explanation
Indices: 337100--337169 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 13
337090 TCCTTTTGGG
337100 TATACCTTTT-AA
1 TATACCTTTTCAA
*
337112 TAATATCC-TTTCGTA
1 T-ATA-CCTTTTC-AA
337127 TATACCTTTTCAA
1 TATACCTTTTCAA
337140 TTATATCC-TTTCGAA
1 -TATA-CCTTTTC-AA
337155 TATACCTTTTCAA
1 TATACCTTTTCAA
337168 TA
1 TA
337170 ATATATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
12 1 0.02
13 15 0.32
14 25 0.53
15 6 0.13
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.47
Consensus pattern (13 bp):
TATACCTTTTCAA
Found at i:343289 original size:19 final size:18
Alignment explanation
Indices: 343267--343303 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
343257 AATTCTCAAT
343267 AAATAAATTATTAAAATTA
1 AAATAAATT-TTAAAATTA
*
343286 AAATATATTTTAAAATTA
1 AAATAAATTTTAAAATTA
343304 TTTTTTGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATAAATTTTAAAATTA
Found at i:349269 original size:19 final size:19
Alignment explanation
Indices: 349237--349273 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
349227 CAGAAAAACT
* *
349237 TTTGTTTTTTTTATTTTTC
1 TTTGTGTTTCTTATTTTTC
349256 TTTGTGTTTCTTATTTTT
1 TTTGTGTTTCTTATTTTT
349274 ATTTTGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.81
Consensus pattern (19 bp):
TTTGTGTTTCTTATTTTTC
Found at i:350877 original size:115 final size:115
Alignment explanation
Indices: 350675--350905 Score: 462
Period size: 115 Copynumber: 2.0 Consensus size: 115
350665 TGATTTTGGG
350675 ATTCATTTACTATTTTTTCCCTAATATTACATGAAGTGGCGAAGCGTAGTGGAGACATGGCCCCC
1 ATTCATTTACTATTTTTTCCCTAATATTACATGAAGTGGCGAAGCGTAGTGGAGACATGGCCCCC
350740 ATAAAATGATAGATTTTTAATTTAGGTCTTTTATAATTTATAAACTTTTA
66 ATAAAATGATAGATTTTTAATTTAGGTCTTTTATAATTTATAAACTTTTA
350790 ATTCATTTACTATTTTTTCCCTAATATTACATGAAGTGGCGAAGCGTAGTGGAGACATGGCCCCC
1 ATTCATTTACTATTTTTTCCCTAATATTACATGAAGTGGCGAAGCGTAGTGGAGACATGGCCCCC
350855 ATAAAATGATAGATTTTTAATTTAGGTCTTTTATAATTTATAAACTTTTA
66 ATAAAATGATAGATTTTTAATTTAGGTCTTTTATAATTTATAAACTTTTA
350905 A
1 A
350906 ATTAGCAGTG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.40
Consensus pattern (115 bp):
ATTCATTTACTATTTTTTCCCTAATATTACATGAAGTGGCGAAGCGTAGTGGAGACATGGCCCCC
ATAAAATGATAGATTTTTAATTTAGGTCTTTTATAATTTATAAACTTTTA
Found at i:352776 original size:15 final size:15
Alignment explanation
Indices: 352710--352809 Score: 80
Period size: 15 Copynumber: 6.7 Consensus size: 15
352700 GGCTATAGGC
352710 TGCGAGCATGAATGT
1 TGCGAGCATGAATGT
*
352725 TGCGATCACT-AATGT
1 TGCGAGCA-TGAATGT
*
352740 TGCGAGCATGACTAG-
1 TGCGAGCATGAAT-GT
* *
352755 TGTGAGCATTAATGT
1 TGCGAGCATGAATGT
* *
352770 TGCGAGCGCT-AATGC
1 TGCGAGC-ATGAATGT
* *
352785 TGCAAGCGTGAATGT
1 TGCGAGCATGAATGT
352800 TGCGAGCATG
1 TGCGAGCATG
352810 GATGAAGAAC
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
14 3 0.05
15 59 0.91
16 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (15 bp):
TGCGAGCATGAATGT
Found at i:352807 original size:45 final size:45
Alignment explanation
Indices: 352710--352809 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
352700 GGCTATAGGC
* * * *
352710 TGCGAGCATGAATGTTGCGATCACTAATGTTGCGAGCATGACTAG
1 TGCGAGCATGAATGTTGCGAGCACTAATGCTGCAAGCATGAATAG
* * * *
352755 TGTGAGCATTAATGTTGCGAGCGCTAATGCTGCAAGCGTGAAT-G
1 TGCGAGCATGAATGTTGCGAGCACTAATGCTGCAAGCATGAATAG
352799 TTGCGAGCATG
1 -TGCGAGCATG
352810 GATGAAGAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (45 bp):
TGCGAGCATGAATGTTGCGAGCACTAATGCTGCAAGCATGAATAG
Found at i:355271 original size:17 final size:17
Alignment explanation
Indices: 355246--355278 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
355236 GTTTACAATT
355246 AAAAAAAATAAAGCAAC
1 AAAAAAAATAAAGCAAC
*
355263 AAAATAAATAAAGCAA
1 AAAAAAAATAAAGCAA
355279 AGAAAGAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAAAAAATAAAGCAAC
Found at i:358770 original size:21 final size:21
Alignment explanation
Indices: 358721--358770 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
358711 TTAATAAATA
*
358721 TAAAATTACACTTTGGCTCCT
1 TAAAATTGCACTTTGGCTCCT
358742 TAAAATTGCACTTTGGAC-CCT
1 TAAAATTGCACTTTGG-CTCCT
358763 TAAAATTG
1 TAAAATTG
358771 ATAAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (21 bp):
TAAAATTGCACTTTGGCTCCT
Found at i:358921 original size:75 final size:77
Alignment explanation
Indices: 358763--358924 Score: 211
Period size: 75 Copynumber: 2.1 Consensus size: 77
358753 TTTGGACCCT
* * *
358763 TAAAATTGATAAAATTTTGATTTAATCCTTTAAAAATTGTTTTGTTACTATCATAAAAATTACAA
1 TAAAAATGATAAAATTATGATCTAATCCTTTAAAAA----TTTGTTACTATCATAAAAATTACAA
358828 TTTAACTTCGCCCCCC
62 TTTAACTTCGCCCCCC
**
358844 TAAAAATGATAAAATTATGATCTAATCCTTTAAAAA-TT-TTACTATCATAAAAATTATTATTTA
1 TAAAAATGATAAAATTATGATCTAATCCTTTAAAAATTTGTTACTATCATAAAAATTACAATTTA
* *
358907 ACTTCGGCCTCC
66 ACTTCGCCCCCC
358919 TAAAAA
1 TAAAAA
358925 AAATTTATGG
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
75 39 0.53
76 2 0.03
81 33 0.45
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (77 bp):
TAAAAATGATAAAATTATGATCTAATCCTTTAAAAATTTGTTACTATCATAAAAATTACAATTTA
ACTTCGCCCCCC
Found at i:358942 original size:35 final size:35
Alignment explanation
Indices: 358901--358971 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
358891 TAAAAATTAT
358901 TATTTAACTTCGGCCTCCTAAAAAAAATTTATGGC
1 TATTTAACTTCGGCCTCCTAAAAAAAATTTATGGC
*
358936 TATTTAACTTCGGCCTCCTAAAAAAATTTTATGGC
1 TATTTAACTTCGGCCTCCTAAAAAAAATTTATGGC
358971 T
1 T
358972 TCGCTCCTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (35 bp):
TATTTAACTTCGGCCTCCTAAAAAAAATTTATGGC
Found at i:359904 original size:30 final size:30
Alignment explanation
Indices: 359868--359929 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
359858 AAATCTTTTT
*
359868 ATTTTTCCC-CAAAAACTTTTACTCCTTTCC
1 ATTTTTCCCTC-AAAACTTTTACTCCCTTCC
359898 ATTTTTCCCTCAAAACTTTTACTCCCTTCC
1 ATTTTTCCCTCAAAACTTTTACTCCCTTCC
359928 AT
1 AT
359930 CCCACCCCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.44
Consensus pattern (30 bp):
ATTTTTCCCTCAAAACTTTTACTCCCTTCC
Found at i:360259 original size:40 final size:40
Alignment explanation
Indices: 360215--360478 Score: 167
Period size: 40 Copynumber: 6.5 Consensus size: 40
360205 CAAAAATGCC
* * * *
360215 CAAAAAGTAAAGCAATAGAGGCGTTTTTCAATAAACGCCG
1 CAAAAGGTAAAGCAATAGAGGCGCTTTCCCATAAACGCCG
* * * *
360255 CAAAAGGTGAAGTAATAGCA-GCGCTTTCCCATAAACACCAT
1 CAAAAGGTAAAGCAATAG-AGGCGCTTTCCCATAAACGCC-G
* ** *** *
360296 C-AAAGGTAAAAAGCAATAGTGGCATTTATGGGA-AAACACCG
1 CAAAAGGT--AAAGCAATAGAGGCGCTT-TCCCATAAACGCCG
* *
360337 CAAAAGGTAAAGCAATAGCGGCGCTTTACCATAAACGCCG
1 CAAAAGGTAAAGCAATAGAGGCGCTTTCCCATAAACGCCG
* * * ****
360377 CAAAAGGTAAAGACCAATAGCGAC-ATTTATGGTAAAACGCCG
1 CAAAAGGTAAAG--CAATAGAGGCGCTTTCCCAT-AAACGCCG
* * *
360419 CAAAAGGTAAAGCAATAGTGACGCTTTCCCATAAACGCAG
1 CAAAAGGTAAAGCAATAGAGGCGCTTTCCCATAAACGCCG
360459 CAAAAGGTAAATAGCAATAG
1 CAAAAGGT-AA-AGCAATAG
360479 CAATGTTTAT
Statistics
Matches: 174, Mismatches: 36, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
39 2 0.01
40 94 0.54
41 14 0.08
42 62 0.36
43 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (40 bp):
CAAAAGGTAAAGCAATAGAGGCGCTTTCCCATAAACGCCG
Found at i:360340 original size:82 final size:82
Alignment explanation
Indices: 360247--360479 Score: 292
Period size: 82 Copynumber: 2.8 Consensus size: 82
360237 GTTTTTCAAT
* * *
360247 AAACGCCGCAAAAGGTGAAGTAATAGCAGCGCTTTCCCATAAACACCATC-AAAGGTAAAAAGCA
1 AAACGCCGCAAAAGGTAAAGCAATAGCAGCGCTTTCCCATAAAC-CCAGCAAAAGGTAAAAAGCA
* *
360311 ATAGTGGCATTTATGGGA
65 ATAGCGACATTTATGGGA
* * * * *
360329 AAACACCGCAAAAGGTAAAGCAATAGCGGCGCTTTACCATAAACGCC-GCAAAAGGTAAAGACCA
1 AAACGCCGCAAAAGGTAAAGCAATAGCAGCGCTTTCCCATAAAC-CCAGCAAAAGGTAAAAAGCA
*
360393 ATAGCGACATTTATGGTA
65 ATAGCGACATTTATGGGA
* * *
360411 AAACGCCGCAAAAGGTAAAGCAATAG-TGACGCTTTCCCATAAACGCAGCAAAAGGTAAATAGCA
1 AAACGCCGCAAAAGGTAAAGCAATAGCAG-CGCTTTCCCATAAACCCAGCAAAAGGTAAAAAGCA
360475 ATAGC
65 ATAGC
360480 AATGTTTATG
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
81 3 0.02
82 127 0.98
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (82 bp):
AAACGCCGCAAAAGGTAAAGCAATAGCAGCGCTTTCCCATAAACCCAGCAAAAGGTAAAAAGCAA
TAGCGACATTTATGGGA
Found at i:361645 original size:41 final size:41
Alignment explanation
Indices: 361511--361645 Score: 109
Period size: 41 Copynumber: 3.3 Consensus size: 41
361501 ATTAGCGTCG
* * * *
361511 TAGCGGCGTTTATGGGAAAAACAACGCTACAA-GTTAAGCAA
1 TAGCGACGTTTATGGGGAAAATACCGCTA-AAGGTTAAGCAA
* * *
361552 TAGCGACGCTTAT-GAG-AAATCACCG-TAATAGGTAAAG-AGCA
1 TAGCGACGTTTATGGGGAAAAT-ACCGCTAA-AGGTTAAGCA--A
361593 TAAGCGACGTTTATGGGGAAAATACCGCTAAAGGTTAAGCAA
1 T-AGCGACGTTTATGGGGAAAATACCGCTAAAGGTTAAGCAA
*
361635 TAGCGGCGTTT
1 TAGCGACGTTT
361646 TCCCATAAAC
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
38 1 0.01
39 7 0.10
40 9 0.12
41 22 0.30
42 13 0.18
43 13 0.18
44 8 0.11
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (41 bp):
TAGCGACGTTTATGGGGAAAATACCGCTAAAGGTTAAGCAA
Found at i:362504 original size:30 final size:30
Alignment explanation
Indices: 362433--362737 Score: 307
Period size: 30 Copynumber: 10.2 Consensus size: 30
362423 TTTTATTTAA
* * *
362433 AAACTTTTCCAAAATTACA-TTTGACCTCT
1 AAACTTTTCTAAAATTACATTTTAACCCCT
*
362462 AAACTTTCCTAAAATTACATTTTAACCCCT
1 AAACTTTTCTAAAATTACATTTTAACCCCT
* *
362492 AAACATTTCTAAAATTACATTTTAAACCCT
1 AAACTTTTCTAAAATTACATTTTAACCCCT
* *
362522 AAACTTATTC-AAAATTACATTCTAAACCCT
1 AAACTT-TTCTAAAATTACATTTTAACCCCT
* * *
362552 AAATTTCTTC-AAAATTACATTCTAACCACT
1 AAACTT-TTCTAAAATTACATTTTAACCCCT
* * * * *
362582 AAAATTTTCCAAAATTACATTTTTACTCTT
1 AAACTTTTCTAAAATTACATTTTAACCCCT
*
362612 AAACTTTTCTAAAATTATATTTTGAA-CCCT
1 AAACTTTTCTAAAATTACATTTT-AACCCCT
* * * * *
362642 AAAATTTTCCAAAATTACATTTTTACTCTT
1 AAACTTTTCTAAAATTACATTTTAACCCCT
*
362672 AAACTTTTCTAAAATTATATTTTGAA-CCCT
1 AAACTTTTCTAAAATTACATTTT-AACCCCT
* *
362702 AAACTTTTCTAAAATTTCATTTTGACCCC-
1 AAACTTTTCTAAAATTACATTTTAACCCCT
362731 AAACTTT
1 AAACTTT
362738 CTCAATAATT
Statistics
Matches: 229, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
29 29 0.13
30 195 0.85
31 5 0.02
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (30 bp):
AAACTTTTCTAAAATTACATTTTAACCCCT
Done.